Dear RDKit community: I am facing the situation that I would like to attach indices to atoms in a molecule defined by a substructure. The substitution pattern is of importance. Therefore I needed to include the wildcards atoms in my substructure. If I get the atom indices of this substructure, the matched atoms are still included and will be used for attaching indices (see at the end of the attached notebook for an example)
I found a solution how to get rid off the non ring atom. That was straightforward. For the attached atom which is part of another ring I needed to do something differently. I determined the atom indices in each ring with GetRingInfo and then I determined which of these rings is part of the tuple of the atom indices of the pattern. Once determined I can do what I need. The question to you is: Is there another more elegant way of doing it? May be I missed something from the python API? I would appreciate any input. Cheers, Markus
AtomMapping.ipynb
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